Align 4-oxalocrotonate decarboxylase subunit (EC 4.1.1.77) (characterized)
to candidate WP_009397184.1 BLS63_RS10120 2-oxo-3-hexenedioate decarboxylase
Query= metacyc::MONOMER-12752 (264 letters) >NCBI__GCF_900100495.1:WP_009397184.1 Length = 264 Score = 508 bits (1307), Expect = e-149 Identities = 255/264 (96%), Positives = 260/264 (98%) Query: 1 MNRTLNREQVLALAEHIENAELQAHDIHKVTNDYPEMTFADAYTIQWEIRRRKEERGNKI 60 MNRTLNREQVLALAEHIENAELQAHDIHKVTNDYPEMTFADAY IQWEIRRRKE RGNKI Sbjct: 1 MNRTLNREQVLALAEHIENAELQAHDIHKVTNDYPEMTFADAYDIQWEIRRRKEARGNKI 60 Query: 61 VGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEIAVVTKAPL 120 VGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEI+VVTKAPL Sbjct: 61 VGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEISVVTKAPL 120 Query: 121 VGPGCHIGDVIAAVDYVIPTVEVIDSRYENFKFDLISVVADNASSTRYITGGRMANLEDV 180 GPGCHIGDVIAAVDYVIPTVEVIDSRYENFKFDLISVVADNASSTR+ITGG+MANLEDV Sbjct: 121 QGPGCHIGDVIAAVDYVIPTVEVIDSRYENFKFDLISVVADNASSTRFITGGQMANLEDV 180 Query: 181 DLRTLGVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAA 240 DLRTLGVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAA Sbjct: 181 DLRTLGVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAA 240 Query: 241 VAVAPGDNITVRYQGLGSVSARFV 264 V+V PGDNITVRYQGLGSVSARF+ Sbjct: 241 VSVEPGDNITVRYQGLGSVSARFI 264 Lambda K H 0.319 0.136 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 362 Number of extensions: 2 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 264 Length of database: 264 Length adjustment: 25 Effective length of query: 239 Effective length of database: 239 Effective search space: 57121 Effective search space used: 57121 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_009397184.1 BLS63_RS10120 (2-oxo-3-hexenedioate decarboxylase)
to HMM TIGR03218 (dmpH: 4-oxalocrotonate decarboxylase (EC 4.1.1.77))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR03218.hmm # target sequence database: /tmp/gapView.24825.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03218 [M=263] Accession: TIGR03218 Description: catechol_dmpH: 4-oxalocrotonate decarboxylase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-156 505.8 0.3 1.3e-156 505.7 0.3 1.0 1 lcl|NCBI__GCF_900100495.1:WP_009397184.1 BLS63_RS10120 2-oxo-3-hexenedioa Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_009397184.1 BLS63_RS10120 2-oxo-3-hexenedioate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 505.7 0.3 1.3e-156 1.3e-156 1 263 [] 1 263 [. 1 263 [. 1.00 Alignments for each domain: == domain 1 score: 505.7 bits; conditional E-value: 1.3e-156 TIGR03218 1 leltltreqiealaehvenaeleareitkitdeyPdldfadaydiqaeirrrklarGakvvGlkaGlts 69 +++tl+req+ alaeh+enael+a++i+k+t++yP+++fadaydiq+eirrrk+arG+k+vGlk+Glts lcl|NCBI__GCF_900100495.1:WP_009397184.1 1 MNRTLNREQVLALAEHIENAELQAHDIHKVTNDYPEMTFADAYDIQWEIRRRKEARGNKIVGLKMGLTS 69 689****************************************************************** PP TIGR03218 70 kakmkqmGvetpvfGfladyfsvpdggeiktselihPkveaeiafvlkaelkgpgchigdvlaatdfvl 138 +akm+qmGvetp++Gfladyfsvpdgg +++s+lihPk+eaei++v+ka+l+gpgchigdv+aa+d+v+ lcl|NCBI__GCF_900100495.1:WP_009397184.1 70 WAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEISVVTKAPLQGPGCHIGDVIAAVDYVI 138 ********************************************************************* PP TIGR03218 139 pavevidsrykdfkfdlksvvadnassarfvtGgraaavedldlrtlGvvleknGevvalgagaavlGh 207 p+vevidsry++fkfdl+svvadnass+rf+tGg++a++ed+dlrtlGvv+eknGevv+lgagaavlGh lcl|NCBI__GCF_900100495.1:WP_009397184.1 139 PTVEVIDSRYENFKFDLISVVADNASSTRFITGGQMANLEDVDLRTLGVVMEKNGEVVELGAGAAVLGH 207 ********************************************************************* PP TIGR03218 208 paaavamlanllaergeeiPaGslilsggiteavavaaGdsvtvrvqelgsvslrf 263 p+++vamlanllaerge+iPaG++i++ggit+av+v++Gd++tvr+q+lgsvs+rf lcl|NCBI__GCF_900100495.1:WP_009397184.1 208 PLSSVAMLANLLAERGEHIPAGTFIMTGGITAAVSVEPGDNITVRYQGLGSVSARF 263 *******************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (264 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.73 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory